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118_gaps2bed.py
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118_gaps2bed.py
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#-----------------------------------------------------------+
# |
# 118_gaps2bed.py - script takes a fasta file and created bed file with gap co-ordinates |
# |
#-----------------------------------------------------------+
# |
# AUTHOR: Vikas Gupta |
# CONTACT: [email protected] |
# STARTED: 09/06/2013 |
# UPDATED: 09/06/2013 |
# |
# DESCRIPTION: |
# Short script to convert and copy the wheat BACs |
# Run this in the parent dir that the HEX* dirs exist |
# |
# LICENSE: |
# GNU General Public License, Version 3 |
# http://www.gnu.org/licenses/gpl.html |
# |
#-----------------------------------------------------------+
# Example:
# python ~/script/python/100b_fasta2flat.py -i 02_Stegodyphous_cdna.refined.fa.orf.tr_longest_frame
### import modules
import os,sys,getopt, re
### global variables
global infile
### make a logfile
import datetime
now = datetime.datetime.now()
o = open(str(now.strftime("%Y-%m-%d_%H%M."))+'logfile','w')
### write logfile
def logfile(infile):
o.write("Program used: \t\t%s" % "100b_fasta2flat.py"+'\n')
o.write("Program was run at: \t%s" % str(now.strftime("%Y-%m-%d_%H%M"))+'\n')
o.write("Infile used: \t\t%s" % infile+'\n')
def help():
print '''
python 118_gaps2bed.py
-i <ifile> ## fasta file
'''
sys.exit(2)
### main argument to
def options(argv):
global infile
infile = ''
try:
opts, args = getopt.getopt(argv,"hi:",["ifile="])
except getopt.GetoptError:
help()
for opt, arg in opts:
if opt == '-h':
help()
elif opt in ("-i", "--ifile"):
infile = arg
logfile(infile)
def make_bed():
'''
# bed format
chloro 20419 20419 L0843 13 +
chloro 28071 28071 L5618 21 -
'''
o = open(infile+'.gaps.bed','w')
for line in open(infile, 'r'):
line = line.strip()
if len(line) >0 and not line.startswith('#'):
if line.startswith('>'):
chro = line[1:]
pos = 0
start_N = 0
end_N = 0
N_region = False
else:
for char in line:
pos += 1
if pos%1000 == 0:
print 'Processing positions: ', chro, '{:10,.0f}'.format(pos)
if char=='N':
if N_region == True:
end_N += 1
else:
start_N = pos
end_N = pos
N_region = True
else:
if N_region == True:
N_region = False
name=chro+'_'+str(start_N)+'_'+str(end_N)
o.write(chro+'\t'+str(start_N)+'\t'+str(end_N)+'\t'+name+'\t'+'.'+'\t'+'+'+'\n')
o.close()
if __name__ == "__main__":
options(sys.argv[1:])
make_bed()
### close the logfile
o.close()